Contacts of the helix formed by residues 352 - 362 (chain H) in PDB entry 2HAK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 352 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117H GLU* 3.4 7.5 - - - +
118H VAL 4.9 3.4 - - - -
345H ALA* 3.8 7.6 - - - +
350H LYS* 3.0 25.3 - - + +
351H TYR* 1.3 79.7 - - - +
353H GLU* 1.3 65.7 + - + +
354H VAL* 3.0 27.3 + - - +
355H MET* 3.0 16.6 + - - +
356H ALA* 3.1 24.1 + - - +
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Residues in contact with GLU 353 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268E ARG* 5.3 10.2 + - - -
269E ILE 4.3 3.5 - - - +
270E PRO* 4.0 3.9 - - - +
271E PHE* 3.0 42.8 + - + +
51H GLY* 5.8 1.9 - - - -
52H ASN* 2.8 30.9 + - - +
72H HIS* 4.8 0.7 + - - -
117H GLU* 3.0 23.3 + - - +
337H PHE* 4.1 2.6 - - + -
352H ASP* 1.3 78.9 - - + +
354H VAL* 1.3 65.9 + - + +
356H ALA* 3.7 1.9 - - - +
357H THR* 2.5 35.3 + - - -
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Residues in contact with VAL 354 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271E PHE* 4.4 5.8 - - + -
332H MET* 3.3 22.0 - - + +
337H PHE* 3.6 26.7 - - + -
341H GLU* 4.6 15.5 - - + +
342H ILE* 3.7 27.8 - - + +
345H ALA* 3.7 16.2 - - + -
352H ASP* 3.0 18.3 + - - +
353H GLU* 1.3 85.0 - - + +
355H MET* 1.3 70.7 + - - +
356H ALA 3.2 0.4 - - - -
357H THR 3.1 8.5 + - - -
358H TYR* 3.1 8.7 + - - +
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Residues in contact with MET 355 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H LYS* 4.7 1.1 - - - +
116H PHE 4.8 0.2 - - - +
345H ALA* 3.8 13.1 - - + +
346H LEU* 4.0 22.4 - - + -
349H GLN* 3.6 25.1 - - - +
350H LYS 3.7 12.6 - - - -
351H TYR* 3.0 66.4 - - + +
352H ASP* 3.0 12.1 + - - +
354H VAL* 1.3 77.1 - - - +
356H ALA* 1.3 55.6 + - - +
358H TYR* 2.7 24.5 + - - +
359H ILE* 3.0 38.1 + - + +
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Residues in contact with ALA 356 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H TYR* 3.7 6.5 - - - +
72H HIS* 4.9 1.1 - - - +
116H PHE* 3.5 24.4 + - + +
117H GLU* 3.3 26.0 - - + +
352H ASP 3.1 21.3 + - - +
353H GLU 3.7 4.3 - - - +
355H MET* 1.3 76.0 - - - +
357H THR* 1.3 57.9 + - - +
359H ILE* 3.4 4.1 + - - +
360H LEU* 2.7 36.8 + - - +
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Residues in contact with THR 357 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72H HIS* 3.6 21.9 - - + -
74H LEU* 3.6 4.1 - - + +
75H THR* 4.1 15.3 - - + +
332H MET* 3.7 25.1 - - + -
335H MET* 4.3 8.1 - - - -
337H PHE* 3.4 21.8 - - + -
353H GLU 2.5 22.0 + - - -
354H VAL 3.1 6.0 + - - -
355H MET 3.1 0.6 - - - -
356H ALA* 1.3 79.8 - - - +
358H TYR* 1.3 58.2 + - - +
360H LEU* 3.9 1.0 - - - +
361H LEU* 3.0 30.8 + - + +
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Residues in contact with TYR 358 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322H ASP 2.7 28.6 + - - -
323H PHE* 3.9 8.1 - + - -
324H ASN 3.1 2.4 + - - -
325H ASP* 2.8 26.2 + - - +
328H ARG* 2.8 67.7 + - + -
329H ILE* 4.1 17.9 - - + -
332H MET* 3.8 24.9 - - + -
342H ILE* 4.0 10.8 - - + -
346H LEU* 3.7 33.4 - - + -
354H VAL 3.1 11.2 + - - +
355H MET 2.7 10.9 + - - +
357H THR* 1.3 75.3 - - - +
359H ILE* 1.3 60.7 + - + +
361H LEU* 3.3 9.4 + - - -
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Residues in contact with ILE 359 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114H LYS* 4.4 20.9 - - + +
115H LEU 4.4 2.0 - - - +
116H PHE* 3.5 44.4 - - + +
328H ARG* 4.0 6.7 - - - +
346H LEU* 5.1 2.5 - - + -
355H MET* 3.0 47.8 + - + +
356H ALA 3.8 4.5 - - - +
358H TYR* 1.3 77.5 - - + +
360H LEU* 1.3 66.9 + - - +
362H GLY* 2.9 17.5 + - - -
363H ARG* 3.5 10.3 + - - +
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Residues in contact with LEU 360 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53H TYR* 4.2 7.2 - - + +
72H HIS* 3.5 42.4 - - + +
75H THR* 3.9 13.2 - - + +
77H ARG* 3.0 38.8 + - + +
78H GLU 5.4 0.4 - - - +
79H VAL* 4.0 15.0 - - + -
116H PHE* 3.5 49.1 - - + -
356H ALA 2.7 25.1 + - - +
357H THR 4.1 2.9 - - - +
359H ILE* 1.3 73.5 - - - +
361H LEU* 1.3 62.1 + - - +
363H ARG* 3.2 12.5 + - + +
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Residues in contact with LEU 361 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75H THR* 3.8 23.8 - - + -
77H ARG* 3.4 24.9 + - - +
328H ARG* 3.6 29.1 - - + +
331H ILE* 3.9 31.6 - - + -
332H MET* 3.7 31.2 - - + -
335H MET* 4.8 5.2 - - + -
357H THR* 3.0 22.2 + - + +
358H TYR 3.4 6.5 - - - +
359H ILE 3.1 0.4 - - - -
360H LEU* 1.3 78.6 - - - +
362H GLY* 1.3 58.6 + - - +
363H ARG 3.2 0.2 - - - -
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Residues in contact with GLY 362 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328H ARG* 3.4 23.5 - - - +
358H TYR 3.3 4.2 + - - -
359H ILE 2.9 9.5 + - - -
361H LEU* 1.3 77.0 - - - +
363H ARG* 1.3 60.0 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il